I haven't read every post in this thread but I can confirm that there is a difference between old Vardar fans and new ones.
My original Vardars start at their controller set speed on startup whereas my newer models start at full speed and ramp back to the controller set speed.
Its pretty annoying. I assumed it had something to do with the start-stop feature they added in the new versions.
This difference is while connected to my Aquaero.
I believe that MBs fan headers will start at full speed because the system sends 12v before the bios loads and the PWM controls kick in.
The Aquaero is already running before the system starts though, so it is def the fans that are causing it.